comparison galaxy_stubs/CalculateSolvationFreeEnergy.xml @ 2:605370bc1def draft default tip

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2:605370bc1def

<?xml version='1.0' encoding='UTF-8'?>
<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
<!--Proposed Tool Section: [ForceFields]-->
<tool id="CalculateSolvationFreeEnergy" name="CalculateSolvationFreeEnergy" version="1.1.0">
  <description>calculate solvation free energy of a protein using AMBER </description>
  <macros>
    <token name="@EXECUTABLE@">CalculateSolvationFreeEnergy</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>CalculateSolvationFreeEnergy

#if $param_pdb:
  -pdb $param_pdb
#end if
#if $param_epsilon_medium:
  -epsilon_medium $param_epsilon_medium
#end if
#if $param_epsilon_vacuum:
  -epsilon_vacuum $param_epsilon_vacuum
#end if
</command>
  <inputs>
    <param name="param_pdb" type="data" format="pdb" optional="False" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="input pdb file" help="(-pdb) "/>
    <param name="param_epsilon_medium" type="float" value="0.0" label="dielectric constant in medium" help="(-epsilon_medium) "/>
    <param name="param_epsilon_vacuum" type="float" value="1.0" label="dielectric constant in vacuum" help="(-epsilon_vacuum) "/>
  </inputs>
  <expand macro="advanced_options"/>
  <outputs>
    <data name="param_stdout" format="text" label="Output from stdout"/>
  </outputs>
  <help>This tool computes the solvation free energy of a pdb file using the Jackson-Sternberg approach (bonded energy using a force field and a non bonded energy (electrostatics only) by solving the Poisson-Boltzmann equation. Parameters are the dielectric constants for the medium (-epsilon_medium) and the vacuum (-epsilon_vacuum).

</help>
</tool>